11-122418637-T-C

Variant names:

• chr11-122418637-T-C
• rs580069
• ENST00000526674.2:n.180+4055A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000526674.2(MIR100HG):​n.180+4055A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,026 control chromosomes in the GnomAD database, including 4,856 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (4856 hom., cov: 32)
• Consequence: MIR100HG ENST00000526674.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 3 publications found

Genes affected

MIR100HG (HGNC:39522): (mir-100-let-7a-2-mir-125b-1 cluster host gene) This gene produces long non-coding RNAs that act as regulators of cell proliferation. Alternative promoter usage and splicing results in multiple transcript variants. Some transcript variants may promote growth, while others may act to negatively regulate cell division. [provided by RefSeq, May 2016]

ENSG00000301744 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_137179.1	n.180+4055A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000526674.2	n.180+4055A>G		intron_variant	Intron 1 of 1	5
MIR100HG	ENST00000533109.6	n.433+120842A>G		intron_variant	Intron 3 of 6	5
MIR100HG	ENST00000637700.1	n.116+34979A>G		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37483 AN: 151908 Hom.: 4846 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.247 AC: 37515 AN: 152026 Hom.: 4856 Cov.: 32 AF XY: 0.247 AC XY: 18341 AN XY: 74294

African (AFR) AF: 0.291 AC: 12050 AN: 41464

American (AMR) AF: 0.257 AC: 3922 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 917 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1566 AN: 5152

South Asian (SAS) AF: 0.302 AC: 1453 AN: 4812

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10566

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14544 AN: 67982

Other (OTH) AF: 0.231 AC: 489 AN: 2116

Alfa AF: 0.224 Hom.: 6473

Bravo AF: 0.250

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs580069; hg19: chr11-122289345;